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I am currently using rsnapshot to backup my sites. It makes it super easy to take incremental backups, and only stores a new copy of a file when it has changed. It doesn't do delta changes though, so even if a file only changes by 1 byte, it will store a completely new copy of the file. Otherwise it uses hard links to save on disk space. The copying is done using rsync, meaning that you can back up remote sites easily as well!

The beauty of this system is that it's super easy to restore from backups... just use the regular old 'cp -r' function.

It works really well for us - we host a large number of Joomla sites, where the core files almost never change. We have our main backup repository on an Amazon EBS volume, which mirrors itself to our office server nightly.

It does use a fair number if inodes though (since everything is a link) so you'll probably want to keep an eye on that (use 'df -i' to see the usage of inodes) or reformat a partition. And there's no encryption for the backup files. It does make its remote backups through ssh though so that's encrypted.